v2.7.1

Full Changelog: v2.6.2...v2.7.1

2.7.1

• Breaking change: File hierarchy now follows what is recommended in the snakemake documentation. Rules are now in individual files.
• Breaking change: profiles/ moved to profile/ (sorry). And local profiles are now named "default".
• Busco runs in protein mode, reusing .faa from prokka (or bakta - see further down). Should result in speedup.
• Added Panaroo, removed Roary.
• For dbcan, only the substrates are shown in the dynamic report.
• Gtdb updated to release 220.0
• Add bakta.
• User can specify whether to use prokka or bakta to create annotation that is used for dbcan, interproscan diamond_kegg, busco. This can be set using --config annotator=bakta or by changing the permanent parameter in config/config.yaml.
• Add eggnog
• rename benchmark files from individual->Sample
• Add antismash. Uses .gbk from prokka.
• report_subpipeline renamed to dynamic_report
• Dynamic report is now run by the ./asscom2 binary instead of using onsuccess/onerror.
• Minor fixes.
• Software versions and database versions are written to hidden files within output directories.
• Added dynamic parameters to prokka and iqtree to the config file.
• Added support for a "fofn" which is a file of file names. In the tseemann style, it defines which input genomes to process.
• Use KEGG KO from eggnog in kegg_pathway. If this doesn't work well I'll consider re-implementing kofam_scan which was removed long time back. Now a_class and b_class are "class" and "group".
• Implemented a way to set the output directory which now defaults to the old static "results_ac2".
• Implemented TreeCluster that on the 4.5% and 10% basis defines clusters on the mashtree distances so the user can easily get an impression on the relative differences between samples.
• Fix an error that makes snp-dists results not show up in the report. (Thanks to @AstaLaugesen)
• Added documentation over at https://assemblycomparator2.readthedocs.io/en/latest/

v2.6.2

Full Changelog: v2.6.1...v2.6.2

2.6.2

• Fix wrong path for dbcan results (not yet implemented in report)
• Downgrade diamond 2.1.8 due to segfault in newest version (2.1.9) bbuchfink/diamond#785

---

v2.6.1

Full Changelog: v2.5.18...v2.6.1

2.6.1

• Remove Kraken2, hence new minor version. Kraken2 really only makes sense on reads.
• Roary as a checkpoint, to only continue with iqtree, fasttree and snp-dists if the core genome is non-empty.
• conda yaml for wget. TODO, carry over to dbcan download as well.

---

v2.5.18

Full Changelog: v2.5.17...v2.5.18

2.5.18

• Support for weird characters in input files. #31
• Support for adding input files from other directories. #58
• Minor bugfixes. #77
• Test battery is being developed. (https://github.com/cmkobel/ac2-test-battery)

---

v2.5.17

Full Changelog: v2.5.16...v2.5.17

• Forced recompilation of docker image did not fix issue #74. This patch has equivalent .yaml-files to version 2.5.14, which means that the old (working) docker image will be compatible.

---

v2.5.15

Full Changelog: v2.5.14...v2.5.15

Dependency snakemake was refactored, so I had to limit the version.

---

v2.5.14

Full Changelog: v2.5.13...v2.5.14

Missing motulizer yaml in docker image.

---

v2.5.10

Full Changelog: v2.5.9...v2.5.10

Supports iqtree.

---

v2.5.9

Full Changelog: v2.5.8...v2.5.9

2.5.9

• Fixed an error where checkm2 would fail setting the download location internally when running asscom2 using the apptainer/docker container. chklovski/CheckM2#73

v2.5.8

Full Changelog: v2.5.7...v2.5.8

2.5.8

• Fixed an error where a different version of the docker image would be pulled for the report subpipeline